In previous work we showed that alerting can induce a global processing bias (Weinbach & Henik, 2011). However, because saliency is often confounded in processing of global features, the present work aimed to investigate the impact of alerting on perceptual processing while controlling for saliency. As in our previous work, participants were presented with a large arrow (global level) comprised of smaller arrows (local level) pointing in the same or opposite directions and had to indicate the direction of the large or small arrows in different blocks. Saliency of the global and local levels was manipulated, creating global-salient and local-salient conditions. Auditory alerting signals were presented in half of the trials prior to the target. Results revealed a double dissociation in the effects of alerting on global/local interference effects as a function of saliency. In a global-salient condition, alerting increased global interference and decreased local interference. In a local-salient condition, alerting reduced global interference and increased local interference. These findings indicate that alerting acts to increase processing of salient visual events, irrespective of the activated perceptual processing mode. In addition, these results challenge previous theories suggesting that alerting acts to increase conflict interference. We showed that alerting can increase or decrease cognitive conflict based on perceptual saliency. We argue that alerting is an adaptive mechanism that diverts attention to salient events, but comes at a cost when selective attention to less salient details is required.